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Help CCAFS with regenerating some item thumbnails after they uploaded new PDFs to some items on CGSpace
A user on the dspace-tech mailing list offered some suggestions for troubleshooting the problem with the inability to delete certain items
Apparently if the item is in the workflowitem table it is submitted to a workflow
And if it is in the workspaceitem table it is in the pre-submitted state
2019-05-05 15:45:12 +02:00
The item seems to be in a pre-submitted state, so I tried to delete it from there:
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dspace=# DELETE FROM workspaceitem WHERE item_id=74648;
DELETE 1
But after this I tried to delete the item from the XMLUI and it is still present…
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< meta name = "twitter:title" content = "May, 2019" / >
< meta name = "twitter:description" content = "2019-05-01
Help CCAFS with regenerating some item thumbnails after they uploaded new PDFs to some items on CGSpace
A user on the dspace-tech mailing list offered some suggestions for troubleshooting the problem with the inability to delete certain items
Apparently if the item is in the workflowitem table it is submitted to a workflow
And if it is in the workspaceitem table it is in the pre-submitted state
2019-05-05 15:45:12 +02:00
The item seems to be in a pre-submitted state, so I tried to delete it from there:
2019-05-01 10:53:26 +02:00
dspace=# DELETE FROM workspaceitem WHERE item_id=74648;
DELETE 1
But after this I tried to delete the item from the XMLUI and it is still present…
"/>
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2019-10-11 10:19:42 +02:00
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< p class = "lead blog-description" dir = "auto" > Documenting day-to-day work on the < a href = "https://cgspace.cgiar.org" > CGSpace< / a > repository.< / p >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2019-05/" > May, 2019< / a > < / h2 >
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< time datetime = "2019-05-01T07:37:43+03:00" > Wed May 01, 2019< / time >
in
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< / header >
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< h2 id = "2019-05-01" > 2019-05-01< / h2 >
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< ul >
< li > Help CCAFS with regenerating some item thumbnails after they uploaded new PDFs to some items on CGSpace< / li >
< li > A user on the dspace-tech mailing list offered some suggestions for troubleshooting the problem with the inability to delete certain items
< ul >
< li > Apparently if the item is in the < code > workflowitem< / code > table it is submitted to a workflow< / li >
< li > And if it is in the < code > workspaceitem< / code > table it is in the pre-submitted state< / li >
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< / ul >
< / li >
< li > The item seems to be in a pre-submitted state, so I tried to delete it from there:< / li >
< / ul >
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< pre tabindex = "0" > < code > dspace=# DELETE FROM workspaceitem WHERE item_id=74648;
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DELETE 1
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< / code > < / pre > < ul >
< li > But after this I tried to delete the item from the XMLUI and it is < em > still< / em > present… < / li >
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< / ul >
< ul >
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< li > I managed to delete the problematic item from the database
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< ul >
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< li > First I deleted the item’ s bitstream in XMLUI and then ran < code > dspace cleanup -v< / code > to remove it from the assetstore< / li >
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< li > Then I ran the following SQL:< / li >
< / ul >
< / li >
< / ul >
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< pre tabindex = "0" > < code > dspace=# DELETE FROM metadatavalue WHERE resource_id=74648;
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dspace=# DELETE FROM workspaceitem WHERE item_id=74648;
dspace=# DELETE FROM item WHERE item_id=74648;
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< / code > < / pre > < ul >
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< li > Now the item is (hopefully) really gone and I can continue to troubleshoot the issue with REST API’ s < code > /items/find-by-metadata-value< / code > endpoint
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< ul >
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< li > Of course I run into another HTTP 401 error when I continue trying the LandPortal search from last month:< / li >
< / ul >
< / li >
< / ul >
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< pre tabindex = "0" > < code > $ curl -f -H " Content-Type: application/json" -X POST " http://localhost:8080/rest/items/find-by-metadata-field" -d ' {" key" :" cg.subject.cpwf" , " value" :" WATER MANAGEMENT" ," language" : " en_US" }'
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curl: (22) The requested URL returned error: 401 Unauthorized
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< / code > < / pre > < ul >
< li > The DSpace log shows the item ID (because I modified the error text):< / li >
< / ul >
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< pre tabindex = "0" > < code > 2019-05-01 11:41:11,069 ERROR org.dspace.rest.ItemsResource @ User(anonymous) has not permission to read item(id=77708)!
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< / code > < / pre > < ul >
< li > If I delete that one I get another, making the list of item IDs so far:
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< ul >
< li > 74648< / li >
< li > 77708< / li >
< li > 85079< / li >
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< / ul >
< / li >
< li > Some are in the < code > workspaceitem< / code > table (pre-submission), others are in the < code > workflowitem< / code > table (submitted), and others are actually approved, but withdrawn…
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< ul >
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< li > This is actually a worthless exercise because the real issue is that the < code > /items/find-by-metadata-value< / code > endpoint is simply designed flawed and shouldn’ t be fatally erroring when the search returns items the user doesn’ t have permission to access< / li >
< li > It would take way too much time to try to fix the fucked up items that are in limbo by deleting them in SQL, but also, it doesn’ t actually fix the problem because some items are < em > submitted< / em > but < em > withdrawn< / em > , so they actually have handles and everything< / li >
< li > I think the solution is to recommend people don’ t use the < code > /items/find-by-metadata-value< / code > endpoint< / li >
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< / ul >
< / li >
< li > CIP is asking about embedding PDF thumbnail images in their RSS feeds again
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< ul >
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< li > They asked in 2018-09 as well and I told them it wasn’ t possible< / li >
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< li > To make sure, I looked at < a href = "https://wiki.lyrasis.org/display/DSPACE/Enable+Media+RSS+Feeds" > the documentation for RSS media feeds< / a > and tried it, but couldn’ t get it to work< / li >
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< li > It seems to be geared towards iTunes and Podcasts… I dunno< / li >
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< / ul >
< / li >
< li > CIP also asked for a way to get an XML file of all their RTB journal articles on CGSpace
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< ul >
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< li > I told them to use the REST API like (where < code > 1179< / code > is the id of the RTB journal articles collection):< / li >
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< / ul >
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< / li >
< / ul >
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< pre tabindex = "0" > < code > https://cgspace.cgiar.org/rest/collections/1179/items?limit=812& expand=metadata
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< / code > < / pre > < h2 id = "2019-05-03" > 2019-05-03< / h2 >
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< ul >
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< li > A user from CIAT emailed to say that CGSpace submission emails have not been working the last few weeks
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< ul >
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< li > I checked the < code > dspace test-email< / code > script on CGSpace and they are indeed failing:< / li >
< / ul >
< / li >
< / ul >
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< pre tabindex = "0" > < code > $ dspace test-email
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About to send test email:
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- To: woohoo@cgiar.org
- Subject: DSpace test email
- Server: smtp.office365.com
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Error sending email:
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- Error: javax.mail.AuthenticationFailedException
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Please see the DSpace documentation for assistance.
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< / code > < / pre > < ul >
< li > I will ask ILRI ICT to reset the password
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< ul >
< li > They reset the password and I tested it on CGSpace< / li >
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< / ul >
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< / li >
< / ul >
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< h2 id = "2019-05-05" > 2019-05-05< / h2 >
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< ul >
< li > Run all system updates on DSpace Test (linode19) and reboot it< / li >
< li > Merge changes into the < code > 5_x-prod< / code > branch of CGSpace:
< ul >
< li > Updates to remove deprecated social media websites (Google+ and Delicious), update Twitter share intent, and add item title to Twitter and email links (< a href = "https://github.com/ilri/DSpace/pull/421" > #421< / a > )< / li >
< li > Add new CCAFS Phase II project tags (< a href = "https://github.com/ilri/DSpace/pull/420" > #420< / a > )< / li >
< li > Add item ID to REST API error logging (< a href = "https://github.com/ilri/DSpace/pull/422" > #422< / a > )< / li >
2019-11-28 16:30:45 +01:00
< / ul >
< / li >
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< li > Re-deploy CGSpace from < code > 5_x-prod< / code > branch< / li >
< li > Run all system updates on CGSpace (linode18) and reboot it< / li >
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< li > Tag version 1.1.0 of the < a href = "https://github.com/ilri/dspace-statistics-api" > dspace-statistics-api< / a > (with Falcon 2.0.0)
< ul >
< li > Deploy on DSpace Test< / li >
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< / ul >
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< / li >
< / ul >
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< h2 id = "2019-05-06" > 2019-05-06< / h2 >
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< ul >
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< li > Peter pointed out that Solr stats are only showing 2019 stats
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< ul >
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< li > I looked at the Solr Admin UI and I see:< / li >
< / ul >
< / li >
< / ul >
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< pre tabindex = "0" > < code > statistics-2018: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
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< / code > < / pre > < ul >
< li > As well as this error in the logs:< / li >
< / ul >
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< pre tabindex = "0" > < code > Caused by: org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2018/data/index/write.lock
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< / code > < / pre > < ul >
< li > Strangely enough, I < em > do< / em > see the statistics-2018, statistics-2017, etc cores in the Admin UI… < / li >
< li > I restarted Tomcat a few times (and even deleted all the Solr write locks) and at least five times there were issues loading one statistics core, causing the Atmire stats to be incomplete
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< ul >
< li > Also, I tried to increase the < code > writeLockTimeout< / code > in < code > solrconfig.xml< / code > from the default of 1000ms to 10000ms< / li >
< li > Eventually the Atmire stats started working, despite errors about “ Error opening new searcher” in the Solr Admin UI< / li >
< li > I wrote to the dspace-tech mailing list again on the thread from March, 2019< / li >
2019-11-28 16:30:45 +01:00
< / ul >
< / li >
< li > There were a few alerts from UptimeRobot about CGSpace going up and down this morning, along with an alert from Linode about 596% load
2019-05-06 14:41:40 +02:00
< ul >
< li > Looking at the Munin stats I see an exponential rise in DSpace XMLUI sessions, firewall activity, and PostgreSQL connections this morning:< / li >
< / ul >
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< / li >
< / ul >
< p > < img src = "/cgspace-notes/2019/05/2019-05-06-jmx_dspace_sessions-day.png" alt = "CGSpace XMLUI sessions day" > < / p >
< p > < img src = "/cgspace-notes/2019/05/2019-05-06-fw_conntrack-day.png" alt = "linode18 firewall connections day" > < / p >
< p > < img src = "/cgspace-notes/2019/05/2019-05-06-postgres_connections_db-day.png" alt = "linode18 postgres connections day" > < / p >
< p > < img src = "/cgspace-notes/2019/05/2019-05-06-cpu-day.png" alt = "linode18 CPU day" > < / p >
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< ul >
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< li > The number of unique sessions today is < em > ridiculously< / em > high compared to the last few days considering it’ s only 12:30PM right now:< / li >
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< / ul >
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< pre tabindex = "0" > < code > $ grep -o -E ' session_id=[A-Z0-9]{32}' dspace.log.2019-05-06 | sort | uniq | wc -l
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101108
2022-03-04 13:30:06 +01:00
$ grep -o -E ' session_id=[A-Z0-9]{32}' dspace.log.2019-05-05 | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
14618
2022-03-04 13:30:06 +01:00
$ grep -o -E ' session_id=[A-Z0-9]{32}' dspace.log.2019-05-04 | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
14946
2022-03-04 13:30:06 +01:00
$ grep -o -E ' session_id=[A-Z0-9]{32}' dspace.log.2019-05-03 | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
6410
2022-03-04 13:30:06 +01:00
$ grep -o -E ' session_id=[A-Z0-9]{32}' dspace.log.2019-05-02 | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
7758
2022-03-04 13:30:06 +01:00
$ grep -o -E ' session_id=[A-Z0-9]{32}' dspace.log.2019-05-01 | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
20528
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > The number of unique IP addresses from 2 to 6 AM this morning is already several times higher than the average for that time of the morning this past week:< / li >
< / ul >
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< pre tabindex = "0" > < code > # zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E ' 06/May/2019:(02|03|04|05|06)' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
7127
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep -E ' 05/May/2019:(02|03|04|05|06)' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
1231
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/access.log.2.gz /var/log/nginx/access.log.3.gz | grep -E ' 04/May/2019:(02|03|04|05|06)' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
1255
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/access.log.3.gz /var/log/nginx/access.log.4.gz | grep -E ' 03/May/2019:(02|03|04|05|06)' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
1736
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/access.log.4.gz /var/log/nginx/access.log.5.gz | grep -E ' 02/May/2019:(02|03|04|05|06)' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
1573
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/access.log.5.gz /var/log/nginx/access.log.6.gz | grep -E ' 01/May/2019:(02|03|04|05|06)' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
1410
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Just this morning between the hours of 2 and 6 the number of unique sessions was < em > very< / em > high compared to previous mornings:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ cat dspace.log.2019-05-06 | grep -E ' 2019-05-06 (02|03|04|05|06):' | grep -o -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
83650
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-05 | grep -E ' 2019-05-05 (02|03|04|05|06):' | grep -o -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
2547
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-04 | grep -E ' 2019-05-04 (02|03|04|05|06):' | grep -o -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
2574
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-03 | grep -E ' 2019-05-03 (02|03|04|05|06):' | grep -o -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
2911
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-02 | grep -E ' 2019-05-02 (02|03|04|05|06):' | grep -o -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
2704
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-01 | grep -E ' 2019-05-01 (02|03|04|05|06):' | grep -o -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
3699
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Most of the requests were GETs:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # cat /var/log/nginx/{access,library-access}.log /var/log/nginx/{access,library-access}.log.1 | grep -E ' 06/May/2019:(02|03|04|05|06)' | grep -o -E " (GET|HEAD|POST|PUT)" | sort | uniq -c | sort -n
2019-11-28 16:30:45 +01:00
1 PUT
98 POST
2845 HEAD
98121 GET
< / code > < / pre > < ul >
2020-01-27 15:20:44 +01:00
< li > I’ m not exactly sure what happened this morning, but it looks like some legitimate user traffic—perhaps someone launched a new publication and it got a bunch of hits?< / li >
2019-11-28 16:30:45 +01:00
< li > Looking again, I see 84,000 requests to < code > /handle< / code > this morning (not including logs for library.cgiar.org because those get HTTP 301 redirect to CGSpace and appear here in < code > access.log< / code > ):< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E ' 06/May/2019:(02|03|04|05|06)' | grep -c -o -E " /handle/[0-9]+/[0-9]+"
2019-05-06 14:41:40 +02:00
84350
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > But it would be difficult to find a pattern for those requests because they cover 78,000 < em > unique< / em > Handles (ie direct browsing of items, collections, or communities) and only 2,492 discover/browse (total, not unique):< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E ' 06/May/2019:(02|03|04|05|06)' | grep -o -E " /handle/[0-9]+/[0-9]+ HTTP" | sort | uniq | wc -l
2019-05-06 14:41:40 +02:00
78104
2022-03-04 13:30:06 +01:00
# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E ' 06/May/2019:(02|03|04|05|06)' | grep -o -E " /handle/[0-9]+/[0-9]+/(discover|browse)" | wc -l
2019-05-06 14:41:40 +02:00
2492
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > In other news, I see some IP is making several requests per second to the exact same REST API endpoints, for example:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # grep /rest/handle/10568/3703?expand=all rest.log | awk ' {print $1}' | sort | uniq -c
2019-11-28 16:30:45 +01:00
3 2a01:7e00::f03c:91ff:fe0a:d645
113 63.32.242.35
< / code > < / pre > < ul >
2020-02-24 18:15:05 +01:00
< li > According to < a href = "https://viewdns.info/reverseip/?host=63.32.242.35&t=1" > viewdns.info< / a > that server belongs to Macaroni Brothers
2019-05-06 14:41:40 +02:00
< ul >
< li > The user agent of their non-REST API requests from the same IP is Drupal< / li >
< li > This is one very good reason to limit REST API requests, and perhaps to enable caching via nginx< / li >
2019-05-06 10:50:57 +02:00
< / ul >
2019-11-28 16:30:45 +01:00
< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-07" > 2019-05-07< / h2 >
2019-05-07 15:51:55 +02:00
< ul >
2019-11-28 16:30:45 +01:00
< li > The total number of unique IPs on CGSpace yesterday was almost 14,000, which is several thousand higher than previous day totals:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # zcat --force /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep -E ' 06/May/2019' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
13969
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/access.log.2.gz /var/log/nginx/access.log.3.gz | grep -E ' 05/May/2019' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
5936
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/access.log.3.gz /var/log/nginx/access.log.4.gz | grep -E ' 04/May/2019' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
6229
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/access.log.4.gz /var/log/nginx/access.log.5.gz | grep -E ' 03/May/2019' | awk ' {print $1}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
8051
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Total number of sessions yesterday was < em > much< / em > higher compared to days last week:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > $ cat dspace.log.2019-05-06 | grep -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
144160
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-05 | grep -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
57269
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-04 | grep -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
58648
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-03 | grep -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
27883
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-02 | grep -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
26996
2022-03-04 13:30:06 +01:00
$ cat dspace.log.2019-05-01 | grep -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-07 15:51:55 +02:00
61866
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > The usage statistics seem to agree that yesterday was crazy:< / li >
2019-05-07 15:51:55 +02:00
< / ul >
2019-11-28 16:30:45 +01:00
< p > < img src = "/cgspace-notes/2019/05/2019-05-07-atmire-usage-week.png" alt = "Atmire Usage statistics spike 2019-05-06" > < / p >
2019-05-07 15:51:55 +02:00
< ul >
< li > Sarah from RTB asked me about the RSS / XML link for the the CGIAR.org website again
< ul >
< li > Apparently Sam Stacey is trying to add an RSS feed so the items get automatically syndicated to the CGIAR website< / li >
< li > I send her the link to the collection RSS feed< / li >
2019-11-28 16:30:45 +01:00
< / ul >
< / li >
2019-05-07 15:51:55 +02:00
< li > Add requests cache to < code > resolve-addresses.py< / code > script< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-08" > 2019-05-08< / h2 >
2019-05-08 14:33:15 +02:00
< ul >
2019-11-28 16:30:45 +01:00
< li > A user said that CGSpace emails have stopped sending again
2019-05-08 14:33:15 +02:00
< ul >
2019-11-28 16:30:45 +01:00
< li > Indeed, the < code > dspace test-email< / code > script is showing an authentication failure:< / li >
< / ul >
< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > $ dspace test-email
2019-05-08 14:33:15 +02:00
About to send test email:
2019-11-28 16:30:45 +01:00
- To: wooooo@cgiar.org
- Subject: DSpace test email
- Server: smtp.office365.com
2019-05-08 14:33:15 +02:00
Error sending email:
2019-11-28 16:30:45 +01:00
- Error: javax.mail.AuthenticationFailedException
2019-05-08 14:33:15 +02:00
Please see the DSpace documentation for assistance.
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > I checked the settings and apparently I had updated it incorrectly last week after ICT reset the password< / li >
2020-01-27 15:20:44 +01:00
< li > Help Moayad with certbot-auto for Let’ s Encrypt scripts on the new AReS server (linode20)< / li >
2019-11-28 16:30:45 +01:00
< li > Normalize all < code > text_lang< / code > values for metadata on CGSpace and DSpace Test (as I had tested last month):< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > UPDATE metadatavalue SET text_lang=' en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN (' ethnob' , ' en' , ' *' , ' E.' , ' ' );
UPDATE metadatavalue SET text_lang=' en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IS NULL;
UPDATE metadatavalue SET text_lang=' es_ES' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN (' es' , ' spa' );
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Send Francesca Giampieri from Bioversity a CSV export of all their items issued in 2018
2019-05-08 14:33:15 +02:00
< ul >
< li > They will be doing a migration of 1500 items from their TYPO3 database into CGSpace soon and want an example CSV with all required metadata columns< / li >
< / ul >
2019-11-28 16:30:45 +01:00
< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-10" > 2019-05-10< / h2 >
2019-05-10 16:27:11 +02:00
< ul >
< li > I finally had time to analyze the 7,000 IPs from the major traffic spike on 2019-05-06 after several runs of my < code > resolve-addresses.py< / code > script (ipapi.co has a limit of 1,000 requests per day)< / li >
< li > Resolving the unique IP addresses to organization and AS names reveals some pretty big abusers:
< ul >
< li > 1213 from Region40 LLC (AS200557)< / li >
< li > 697 from Trusov Ilya Igorevych (AS50896)< / li >
< li > 687 from UGB Hosting OU (AS206485)< / li >
< li > 620 from UAB Rakrejus (AS62282)< / li >
< li > 491 from Dedipath (AS35913)< / li >
< li > 476 from Global Layer B.V. (AS49453)< / li >
< li > 333 from QuadraNet Enterprises LLC (AS8100)< / li >
< li > 278 from GigeNET (AS32181)< / li >
< li > 261 from Psychz Networks (AS40676)< / li >
< li > 196 from Cogent Communications (AS174)< / li >
< li > 125 from Blockchain Network Solutions Ltd (AS43444)< / li >
< li > 118 from Silverstar Invest Limited (AS35624)< / li >
2019-11-28 16:30:45 +01:00
< / ul >
< / li >
< li > All of the IPs from these networks are using generic user agents like this, but MANY more, and they change many times:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > " Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/50.0.2703.0 Safari/537.36"
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > I found a < a href = "https://www.qurium.org/alerts/azerbaijan/azerbaijan-and-the-region40-ddos-service/" > blog post from 2018 detailing an attack from a DDoS service< / a > that matches our pattern exactly< / li >
< li > They specifically mention:< / li >
2019-05-10 16:27:11 +02:00
< / ul >
2019-11-28 16:30:45 +01:00
<!-- raw HTML omitted -->
2019-05-10 16:27:11 +02:00
< ul >
2019-05-12 09:39:10 +02:00
< li > So this was definitely an attack of some sort… only God knows why< / li >
2020-01-27 15:20:44 +01:00
< li > I noticed a few new bots that don’ t use the word “ bot” in their user agent and therefore don’ t match Tomcat’ s Crawler Session Manager Valve:
2019-05-10 16:27:11 +02:00
< ul >
< li > < code > Blackboard Safeassign< / code > < / li >
2019-05-12 12:59:44 +02:00
< li > < code > Unpaywall< / code > < / li >
2019-05-10 16:27:11 +02:00
< / ul >
2019-11-28 16:30:45 +01:00
< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-12" > 2019-05-12< / h2 >
2019-05-12 09:39:10 +02:00
< ul >
2019-11-28 16:30:45 +01:00
< li > I see that the Unpaywall bot is resonsible for a few thousand XMLUI sessions every day (IP addresses come from nginx access.log):< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > $ cat dspace.log.2019-05-11 | grep -E ' ip_addr=(100.26.206.188|100.27.19.233|107.22.98.199|174.129.156.41|18.205.243.110|18.205.245.200|18.207.176.164|18.207.209.186|18.212.126.89|18.212.5.59|18.213.4.150|18.232.120.6|18.234.180.224|18.234.81.13|3.208.23.222|34.201.121.183|34.201.241.214|34.201.39.122|34.203.188.39|34.207.197.154|34.207.232.63|34.207.91.147|34.224.86.47|34.227.205.181|34.228.220.218|34.229.223.120|35.171.160.166|35.175.175.202|3.80.201.39|3.81.120.70|3.81.43.53|3.84.152.19|3.85.113.253|3.85.237.139|3.85.56.100|3.87.23.95|3.87.248.240|3.87.250.3|3.87.62.129|3.88.13.9|3.88.57.237|3.89.71.15|3.90.17.242|3.90.68.247|3.91.44.91|3.92.138.47|3.94.250.180|52.200.78.128|52.201.223.200|52.90.114.186|52.90.48.73|54.145.91.243|54.160.246.228|54.165.66.180|54.166.219.216|54.166.238.172|54.167.89.152|54.174.94.223|54.196.18.211|54.198.234.175|54.208.8.172|54.224.146.147|54.234.169.91|54.235.29.216|54.237.196.147|54.242.68.231|54.82.6.96|54.87.12.181|54.89.217.141|54.89.234.182|54.90.81.216|54.91.104.162)' | grep -E ' session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2019-05-12 12:59:44 +02:00
2206
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > I added “ Unpaywall” to the list of bots in the Tomcat Crawler Session Manager Valve< / li >
< li > Set up nginx to use TLS and proxy pass to NodeJS on the AReS development server (linode20)< / li >
< li > Run all system updates on linode20 and reboot it< / li >
< li > Also, there is 10 to 20% CPU steal on that VM, so I will ask Linode to move it to another host< / li >
< li > Commit changes to the < code > resolve-addresses.py< / code > script to add proper CSV output support< / li >
2019-05-12 09:39:10 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-14" > 2019-05-14< / h2 >
2019-05-14 20:20:49 +02:00
< ul >
< li > Skype with Peter and AgroKnow about CTA story telling modification they want to do on the CTA ICT Update collection on CGSpace
< ul >
< li > I told them they should aim for modifying the collection theme and insert some custom HTML / JS< / li >
< li > I need to send Panagis some documentation about Mirage 2 and the DSpace build process, as well as the Maven settings for build< / li >
< / ul >
2019-11-28 16:30:45 +01:00
< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-15" > 2019-05-15< / h2 >
2019-05-15 17:06:05 +02:00
< ul >
2020-01-27 15:20:44 +01:00
< li > Tezira says she’ s having issues with email reports for approved submissions, but I received an email about collection subscriptions this morning, and I tested with < code > dspace test-email< / code > and it’ s also working… < / li >
2019-05-15 17:06:05 +02:00
< li > Send a list of DSpace build tips to Panagis from AgroKnow< / li >
2019-05-15 23:12:50 +02:00
< li > Finally fix the AReS v2 to work via DSpace Test and send it to Peter et al to give their feedback
< ul >
< li > We had issues with CORS due to Moayad using a hard-coded domain name rather than a relative URL< / li >
2019-05-15 17:06:05 +02:00
< / ul >
2019-11-28 16:30:45 +01:00
< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-16" > 2019-05-16< / h2 >
2019-05-16 17:26:49 +02:00
< ul >
2019-11-28 16:30:45 +01:00
< li > Export a list of all investors (< code > dc.description.sponsorship< / code > ) for Peter to look through and correct:< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 29 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2019-05-16-investors.csv WITH CSV HEADER;
2019-05-16 17:26:49 +02:00
COPY 995
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
2020-01-27 15:20:44 +01:00
< li > Fork the < a href = "https://github.com/icarda-git/AReS" > ICARDA AReS v1 repository< / a > to < a href = "https://github.com/ilri/AReS" > ILRI’ s GitHub< / a > and give access to CodeObia guys
2019-05-16 17:26:49 +02:00
< ul >
< li > The plan is that we develop the v2 code here< / li >
< / ul >
2019-11-28 16:30:45 +01:00
< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-17" > 2019-05-17< / h2 >
2019-05-17 17:46:13 +02:00
< ul >
< li > Peter sent me a bunch of fixes for investors from yesterday< / li >
2019-11-28 16:30:45 +01:00
< li > I did a quick check in Open Refine (trim and collapse whitespace, clean smart quotes, etc) and then applied them on CGSpace:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > $ ./fix-metadata-values.py -i /tmp/2019-05-16-fix-306-Investors.csv -db dspace-u dspace-p ' fuuu' -f dc.description.sponsorship -m 29 -t correct -d
$ ./delete-metadata-values.py -i /tmp/2019-05-16-delete-297-Investors.csv -db dspace -u dspace -p ' fuuu' -m 29 -f dc.description.sponsorship -d
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Then I started a full Discovery re-indexing:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > $ export JAVA_OPTS=" -Dfile.encoding=UTF-8 -Xmx1024m"
2019-05-17 17:46:13 +02:00
$ time schedtool -B -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > I was going to make a new controlled vocabulary of the top 100 terms after these corrections, but I noticed a bunch of duplicates and variations when I sorted them alphabetically< / li >
< li > Instead, I exported a new list and asked Peter to look at it again< / li >
2020-01-27 15:20:44 +01:00
< li > Apply Peter’ s new corrections on DSpace Test and CGSpace:< / li >
2019-11-28 16:30:45 +01:00
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > $ ./fix-metadata-values.py -i /tmp/2019-05-17-fix-25-Investors.csv -db dspace -u dspace -p ' fuuu' -f dc.description.sponsorship -m 29 -t correct -d
$ ./delete-metadata-values.py -i /tmp/2019-05-17-delete-14-Investors.csv -db dspace -u dspace -p ' fuuu' -m 29 -f dc.description.sponsorship -d
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Then I re-exported the sponsors and took the top 100 to update the existing controlled vocabulary (< a href = "https://github.com/ilri/DSpace/pull/423" > #423< / a > )
2019-05-17 21:20:49 +02:00
< ul >
< li > I will deploy the changes on CGSpace the next time we re-deploy< / li >
2019-05-17 17:46:13 +02:00
< / ul >
2019-11-28 16:30:45 +01:00
< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-19" > 2019-05-19< / h2 >
2019-05-24 08:47:52 +02:00
< ul >
< li > Add “ ISI journal” to item view sidebar at the request of Maria Garruccio< / li >
< li > Update < code > fix-metadata-values.py< / code > and < code > delete-metadata-values.py< / code > scripts to add some basic checking of CSV fields and colorize shell output using Colorama< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-24" > 2019-05-24< / h2 >
2019-05-24 08:47:52 +02:00
< ul >
< li > Update AReS README.md on GitHub repository to add a proper introduction, credits, requirements, installation instructions, and legal information< / li >
2019-05-24 11:27:22 +02:00
< li > Update CIP subjects in input forms on CGSpace (< a href = "https://github.com/ilri/DSpace/pull/424" > #424< / a > )< / li >
2019-05-24 08:47:52 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-25" > 2019-05-25< / h2 >
2019-05-25 13:17:27 +02:00
< ul >
< li > Help Abenet proof ten Africa Rice publications
< ul >
< li > Convert some dates to string (from number in Excel)< / li >
< li > Trim whitespace on all fields< / li >
< li > Correct and standardize affiliations< / li >
< li > Validate subject terms against AGROVOC< / li >
< li > Add rights information to all items< / li >
< li > Correct and standardize sponsors< / li >
< / ul >
2019-11-28 16:30:45 +01:00
< / li >
< li > Generate Simple Archive Format bundle with SAFBuilder and import into the < a href = "https://cgspace.cgiar.org/handle/10568/101106" > AfricaRice Articles in Journals< / a > collection on CGSpace:< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > $ dspace import -a -e me@cgiar.org -m 2019-05-25-AfricaRice.map -s /tmp/SimpleArchiveFormat
2019-12-17 13:49:24 +01:00
< / code > < / pre > < h2 id = "2019-05-27" > 2019-05-27< / h2 >
2019-05-27 11:06:48 +02:00
< ul >
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< li > Peter sent me over two thousand corrections for the authors on CGSpace that I had dumped last month
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< ul >
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< li > I proofed them for whitespace and invalid special characters in OpenRefine and then applied them on CGSpace and DSpace Test:< / li >
< / ul >
< / li >
< / ul >
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< pre tabindex = "0" > < code > $ ./fix-metadata-values.py -i /tmp/2019-05-27-fix-2472-Authors.csv -db dspace -u dspace -p ' fuuu' -f dc.contributor.author -m 3 -t corrections -d
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< / code > < / pre > < ul >
< li > Then start a full Discovery re-indexing on each server:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ export JAVA_OPTS=" -Dfile.encoding=UTF-8 -Xmx1024m"
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$ time schedtool -B -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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< / code > < / pre > < ul >
< li > Export new list of all authors from CGSpace database to send to Peter:< / li >
< / ul >
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< pre tabindex = "0" > < code > dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = ' contributor' and qualifier = ' author' ) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/2019-05-27-all-authors.csv with csv header;
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COPY 64871
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< / code > < / pre > < ul >
< li > Run all system updates on DSpace Test (linode19) and reboot it< / li >
< li > Paola from CIAT asked for a way to generate a report of the top keywords for each year of their articles and journals
2019-05-27 11:20:07 +02:00
< ul >
2020-01-27 15:20:44 +01:00
< li > I told them that the best way (even though it’ s low tech) is to work on a CSV dump of the collection< / li >
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< / ul >
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< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2019-05-29" > 2019-05-29< / h2 >
2019-05-29 18:06:52 +02:00
< ul >
< li > A CIMMYT user was having problems registering or logging into CGSpace
< ul >
< li > I tried to register her and it gave an error, then I remembered for CGIAR LDAP users we actually need to just log in and it will automatically create an eperson< / li >
< li > I told her to try to log in with the LDAP login method and let me know what happens (then I can look in the logs too)< / li >
< / ul >
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< / li >
< / ul >
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< h2 id = "2019-05-30" > 2019-05-30< / h2 >
2019-06-02 09:57:51 +02:00
< ul >
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< li > I see the following error in the DSpace log when the user tries to log in with her CGIAR email and password on the LDAP login:< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > 2019-05-30 07:19:35,166 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=A5E0C836AF8F3ABB769FE47107AE1CFF:ip_addr=185.71.4.34:failed_login:no DN found for user sa.saini@cgiar.org
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< / code > < / pre > < ul >
2020-01-27 15:20:44 +01:00
< li > For now I just created an eperson with her personal email address until I have time to check LDAP to see what’ s up with her CGIAR account:< / li >
2019-06-02 09:57:51 +02:00
< / ul >
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< pre tabindex = "0" > < code > $ dspace user -a -m blah@blah.com -g Sakshi -s Saini -p ' sknflksnfksnfdls'
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< / code > < / pre > <!-- raw HTML omitted -->
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< / article >
< / div > <!-- /.blog - main -->
< aside class = "col-sm-3 ml-auto blog-sidebar" >
< section class = "sidebar-module" >
< h4 > Recent Posts< / h4 >
< ol class = "list-unstyled" >
2023-06-02 15:33:48 +02:00
< li > < a href = "/cgspace-notes/2023-06/" > June, 2023< / a > < / li >
2023-05-03 16:10:37 +02:00
< li > < a href = "/cgspace-notes/2023-05/" > May, 2023< / a > < / li >
2023-04-02 08:16:25 +02:00
< li > < a href = "/cgspace-notes/2023-04/" > April, 2023< / a > < / li >
2023-03-01 06:30:25 +01:00
< li > < a href = "/cgspace-notes/2023-03/" > March, 2023< / a > < / li >
2023-02-09 06:50:54 +01:00
< li > < a href = "/cgspace-notes/2023-02/" > February, 2023< / a > < / li >
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< / section >
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< h4 > Links< / h4 >
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< li > < a href = "https://cgspace.cgiar.org" > CGSpace< / a > < / li >
< li > < a href = "https://dspacetest.cgiar.org" > DSpace Test< / a > < / li >
< li > < a href = "https://github.com/ilri/DSpace" > CGSpace @ GitHub< / a > < / li >
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